scholarly journals High-performance, quantum mechanics-based macromolecular x-ray refinement

2014 ◽  
Vol 70 (a1) ◽  
pp. C1446-C1446
Author(s):  
Oleg Borbulevych ◽  
Lance Westerhoff
Keyword(s):  
Quantum Mechanics ◽  
Active Site ◽  
High Performance ◽  
Covalent Bonds ◽  
Metal Centers ◽  
X Ray ◽  
Design And Optimization ◽  
Surrounding Structure ◽  
Lower Strain ◽  
Coordination Spheres

"Modern, structure based drug discovery (SBDD) is dependent upon accurate protein:ligand structure determination and characterization. In conventional x-ray refinement, the geometry of the ligand within the active site is modeled according to the practitioner's beliefs as expressed in the form of stereochemical restraints provided by the ligand library or CIF file. Further, metal centers, bound species, and so on can be difficult to refine correctly without significant human intervention. Our work has addressed this problem through the integration of DivCon6 - a linear scaling, semiempirical, quantum mechanics (SE-QM) functional - with the Phenix refinement package. With Phenix/DivCon[1], SE-QM is used in ""real-time"" during each microcycle over the course of the refinement. With its inclusion of electrostatics, charge transfer, polarization, dispersion, hydrogen bonds, etcetera, this method is a much more rigorous, robust alternative to conventional stereochemical restraints and is better able to accurately model protein:ligand structures without ""tweaking"" any restraints. We report PM6 refinement results for several key examples including structures with metal coordination spheres, covalent bonds, and other exotic protein:ligand chemistry situations. When compared with the originally deposited PDB structures, we found in all cases that QM refinement leads to ligand structures with much lower strain, and in some cases, the improvement is dramatic and as much 10+ fold. At the same time, SE-QM methods are better able to capture the influence of the surrounding structure (e.g. active site) on the ligand. These interactions are particularly interesting in SBDD as they are often the targets for lead design and optimization, and examples that illustrate how these interactions are captured with SE-QM will also be discussed."

A Cross-Scale Characterization of Interface Properties between Carbon Nanotubes and Polymer Matrix

2006 ◽  
Vol 312 ◽  
pp. 217-222 ◽  
Author(s):  
Kausala Mylvaganam ◽  
Liang Chi Zhang
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
High Performance ◽  
Mechanical Deformation ◽  
Polymer Chains ◽  
Interface Properties ◽  
Covalent Bonds ◽  
Scale Characterization

This paper discusses the methods of promoting covalent bonds between polymer and carbon nanotubes to make high performance composites. Such methods involve attachment of chemical moieties (i.e. functional groups) to the sidewalls of carbon nanotubes, introduction of mechanical deformation on nanotubes, or generation of radicals on the polymer chains using free radical generators. The implementation of the latter method is demonstrated at both quantum mechanics and molecular dynamics levels.

scholarly journals Solving an X-Ray Structure of a Bio-Artificial Neurotransmitter Receptor Designed for the Naked-Eye Recognition of Dopamine

2020 ◽  
Author(s):  
Thibaud Rossel ◽  
Bing Zhang ◽  
Raphael Gobat
Keyword(s):  
Chemical Synthesis ◽  
Small Molecules ◽  
Active Site ◽  
Chemical Sensor ◽  
Selective Detection ◽  
Neurotransmitter Receptor ◽  
X Ray ◽  
Naked Eye ◽  
Coordination Spheres ◽  
Eye Recognition

The literature is constellated with a wide variety of chemosensors against a plethora of analytes. This seminal library is used to inspire chemists to improve them using chemical synthesis. However, their optimization via chemical synthesis is a difficult task which takes time without the guarantee of final success.We show here that combinatorial chemistry,the use of first and second coordination spheres and the displacement of indicators united within a protein cavity offers an easy-to-assemble colorimetric bio-chemical sensor. It consists only of commercial chemicals. This colorimetric sensor is highly modular, cheap and evolvable. Its X-ray structure reveals the composition of its active site. This allows to design it rationally for the recognition of dopamine with the naked eye. Our bio-sensor therefore resembles a biological receptor for the recognition of neurotransmitters. Its immediate high adaptability and ability to be evolved can be useful for the selective detection of a wide variety of analytes going from small molecules to microorganisms. This discovery therefore makes it possible to dream of new biotechnological or new immunotherapeutic applications.<br>

Kupfer- und Goldkomplexe von Dithiocarbaminsäureestern. Strukturen von [CuCI(L1)3] · CH2Cl2, [AuCl(L1)2], [CuI(L1)(PPh3)]2 und [Cu2ICuIICl4(L2)2]n (L1 = N-Phenyl-S-methyldithiocarbaminsäureester, L2 = N,N-Dimethyl-S-methyldithiocarbaminsäureester) / Copper and Gold Complexes of Dithiocarbamate Esters. X-Ray Structures of [CuCl(L1)3] · CH2Cl2, [AuCl(L1)2], [CuI(L1)(PPh3)]2 and [Cu2ICuIICl4(L2)2]n (L1 = N-Phenyl-S-methyldithiocarbamate, L2 = N,N-Dimethyl-S-methyldithiocarbamate)

1993 ◽  
Vol 48 (9) ◽  
pp. 1227-1233 ◽  
Author(s):  
Klaus Schulbert ◽  
Rainer Mattes
Keyword(s):  
Mixed Valence ◽  
Chain Structure ◽  
Metal Centers ◽  
X Ray ◽  
X Ray Crystallography ◽  
Square Planar ◽  
Coordination Spheres ◽  
A Chain ◽  
Identity Period ◽  
Mixed Valence Complex

Reactions of N-phenyl-S-methyldithiocarbamate (L1) and N,N-dimethyl-S-methyldithio-carbamate (L2) with CuCl2, [Cu2I2(PPh3)3] and HAuCl4 yield the complexes [CuCl(L1)3] • CH2Cl2 (1), [AuCl(L1)2] (2), [CuI(L1)(PPh3)]2 (3) and [Cu2ICuIICl4(L2)2]n (4). Their structures have been determined by single crystal X-ray crystallography. 1 and 2 are monomeric, with Cu(I) tetrahedrally four-coordinate and Au(I) two-coordinate with an S-Au-S angle of 158.2(1)°. 3 is dimeric with a central CuI2Cu core, the Cu•••Cu distance of which [314.9(1) pm] is rather large. The mixed valence complex 4 has a chain structure with the identity period CuII(μ-Cl)2CuI(μ-S)2CuI(μ-Cl)2. CuI is in a tetrahedral, CuII in a square planar environment. The (μ-S)2 bridged CuI ••• CuI distance is only 259.1(1) pm. The structures of the CuX2Cu cores of 3 and 4 are mainly determined by steric interactions of the donor atoms within the coordination spheres of the metal centers.

scholarly journals Enzyvitands: evolvable biosynthetic and colorimetric chalices

2020 ◽  
Author(s):  
Thibaud Rossel ◽  
Bing Zhang ◽  
Raphael Gobat
Keyword(s):  
Chemical Synthesis ◽  
Small Molecules ◽  
Active Site ◽  
Chemical Sensor ◽  
Colorimetric Sensor ◽  
Selective Detection ◽  
X Ray ◽  
Naked Eye ◽  
Coordination Spheres

The literature is constellated with a wide variety of chemosensors against a plethora of analytes. This seminal library is used to inspire chemists to improve them using chemical synthesis. However, their optimization via chemical synthesis is a difficult task which takes time without the guarantee of final success.We show here that combinatorial chemistry,the use of first and second coordination spheres and the displacement of indicators united within a protein cavity offers an easy-to-assemble colorimetric bio-chemical sensor. It consists only of commercial chemicals. This colorimetric sensor is highly modular, cheap and evolvable. Its X-ray structure reveals the composition of its active site. This allows to design it rationally for the recognition of dopamine with the naked eye. Our bio-sensor therefore resembles a biological receptor for the recognition of neurotransmitters. Its immediate high adaptability and ability to be evolved can be useful for the selective detection of a wide variety of analytes going from small molecules to microorganisms. This discovery therefore makes it possible to dream of new biotechnological or new immunotherapeutic applications.<br>

scholarly journals Enzyvitands: evolvable biosynthetic and colorimetric chalices

2020 ◽  
Author(s):  
Thibaud Rossel ◽  
Bing Zhang ◽  
Raphael Gobat
Keyword(s):  
Chemical Synthesis ◽  
Small Molecules ◽  
Active Site ◽  
Chemical Sensor ◽  
Colorimetric Sensor ◽  
Selective Detection ◽  
X Ray ◽  
Naked Eye ◽  
Coordination Spheres

The literature is constellated with a wide variety of chemosensors against a plethora of analytes. This seminal library is used to inspire chemists to improve them using chemical synthesis. However, their optimization via chemical synthesis is a difficult task which takes time without the guarantee of final success.We show here that combinatorial chemistry,the use of first and second coordination spheres and the displacement of indicators united within a protein cavity offers an easy-to-assemble colorimetric bio-chemical sensor. It consists only of commercial chemicals. This colorimetric sensor is highly modular, cheap and evolvable. Its X-ray structure reveals the composition of its active site. This allows to design it rationally for the recognition of dopamine with the naked eye. Our bio-sensor therefore resembles a biological receptor for the recognition of neurotransmitters. Its immediate high adaptability and ability to be evolved can be useful for the selective detection of a wide variety of analytes going from small molecules to microorganisms. This discovery therefore makes it possible to dream of new biotechnological or new immunotherapeutic applications.<br>

scholarly journals Automated grid-based XFEL diffraction studies of single macromolecular crystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C572-C572
Author(s):  
S Soltis ◽  
Aina Cohen ◽  
Henrik Lemke ◽  
Scott McPhillips ◽  
John Peters ◽  
...  
Keyword(s):  
Active Site ◽  
Visible Absorption ◽  
Structural Investigations ◽  
Metal Centers ◽  
Still Image ◽  
X Ray ◽  
Alignment Procedure ◽  
Additional Information ◽  
Small X ◽  
Effects Of Radiation

A major challenge of structural investigations of metalloproteins at synchrotrons is the damaging effects of radiation exposure. Even small X-ray doses can reduce or initiate reactions at metal centers modifying the active site. For example, in-situ visible absorption spectroscopy measurements have demonstrated that the heme/copper active site in oxidized ba3 cytochrome oxidase (ba3) is compromised during a single X-ray diffraction exposure. The use of ultrashort X-ray pulses at LCLS provides a means to measure high resolution diffraction before these damage processes occur. To this end, experiments were conducted at LCLS using large multiple crystals (> 50 µm) of ba3, hydrogenase and myoglobin. Crystals were mounted in `grids' or loops and flash frozen. The grids hold up to 75 crystals in known locations and are compatible with the Stanford Automounter used to exchange them. Following a semi-automated grid alignment procedure, a fully automated routine was used to position each crystal and collect a series of diffraction images and the Blu-Ice/DCS control system that coordinated with the LCLS EPICS system and XPP DAQ software. Single femtosecond X-ray pulses produced a `damage free' still diffraction image from each crystal. To provide additional information about crystal orientation, a series of pseudo-oscillation images were collected +/- 5.5 degrees spanning the orientation of the still image. For each one degree oscillation image the crystal was exposed to 120 attenuated X-ray pulses. A hard X-ray spectrometer was used to measure the energy spectrum of each individual X-ray pulse. The details and results of these experiments will be presented.

Macroprobe Mode for the Study of Segregation in Steels

1990 ◽  
Vol 48 (2) ◽  
pp. 260-261
Author(s):  
Auclair Gilles ◽  
Benoit Danièle
Keyword(s):  
Mechanical Properties ◽  
Spatial Distribution ◽  
High Performance ◽  
Volume Fraction ◽  
Sheet Steel ◽  
Acquisition Time ◽  
Chemical Information ◽  
X Ray ◽  
Accurate Quantitative Analysis ◽  
Optical Micrographs

During these last 10 years, high performance correction procedures have been developed for classical EPMA, and it is nowadays possible to obtain accurate quantitative analysis even for soft X-ray radiations. It is also possible to perform EPMA by adapting this accurate quantitative procedures to unusual applications such as the measurement of the segregation on wide areas in as-cast and sheet steel products.The main objection for analysis of segregation in steel by means of a line-scan mode is that it requires a very heavy sampling plan to make sure that the most significant points are analyzed. Moreover only local chemical information is obtained whereas mechanical properties are also dependant on the volume fraction and the spatial distribution of highly segregated zones. For these reasons we have chosen to systematically acquire X-ray calibrated mappings which give pictures similar to optical micrographs. Although mapping requires lengthy acquisition time there is a corresponding increase in the information given by image anlysis.

PHAX-SCAN: Functional integration of a Scanning Electron Microscope and an energy-dispersive x-ray analyser

1989 ◽  
Vol 47 ◽  
pp. 56-57
Author(s):  
Marc H. Peeters ◽  
Max T. Otten
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
High Speed ◽  
High Performance ◽  
Functional Integration ◽  
Energy Dispersive ◽  
X Rays ◽  
X Ray ◽  
High Speed Analysis ◽  
Scanning Electron

Over the past decades, the combination of energy-dispersive analysis of X-rays and scanning electron microscopy has proved to be a powerful tool for fast and reliable elemental characterization of a large variety of specimens. The technique has evolved rapidly from a purely qualitative characterization method to a reliable quantitative way of analysis. In the last 5 years, an increasing need for automation is observed, whereby energy-dispersive analysers control the beam and stage movement of the scanning electron microscope in order to collect digital X-ray images and perform unattended point analysis over multiple locations.The Philips High-speed Analysis of X-rays system (PHAX-Scan) makes use of the high performance dual-processor structure of the EDAX PV9900 analyser and the databus structure of the Philips series 500 scanning electron microscope to provide a highly automated, user-friendly and extremely fast microanalysis system. The software that runs on the hardware described above was specifically designed to provide the ultimate attainable speed on the system.

Xenon Trioxide Adducts of O-Donor Ligands; [(CH3)2CO]3XeO3, [(CH3)2SO]3(XeO3)2, (C5H5NO)3(XeO3)2, and [(C6H5)3PO]2XeO3

2018 ◽  
Author(s):  
Katherine Marczenko ◽  
James Goettel ◽  
Gary Schrobilgen
Keyword(s):  
Room Temperature ◽  
Triphenylphosphine Oxide ◽  
Donor Ligands ◽  
Mechanical Shock ◽  
X Ray Diffraction ◽  
X Ray ◽  
Oxygen Coordination ◽  
Xenon Trioxide ◽  
Distorted Octahedra ◽  
Coordination Spheres

Oxygen coordination to the Xe(VI) atom of XeO<sub>3</sub> was observed in its adducts with triphenylphosphine oxide, dimethylsulfoxide, pyridine-N-oxide, and acetone. The crystalline adducts were characterized by low-temperature, single-crystal X-ray diffraction and Raman spectroscopy. Unlike solid XeO<sub>3</sub>, which detonates when mechanically or thermally shocked, the solid [(C<sub>6</sub>H<sub>5</sub>)<sub>3</sub>PO]<sub>2</sub>XeO<sub>3</sub>, [(CH<sub>3</sub>)<sub>2</sub>SO]<sub>3</sub>(XeO<sub>3</sub>)<sub>2</sub>,<sub> </sub>and (C<sub>5</sub>H<sub>5</sub>NO)<sub>3</sub>(XeO<sub>3</sub>)<sub>2</sub> adducts are insensitive to mechanical shock, but undergo rapid deflagration when ignited by a flame. Both [(C<sub>6</sub>H<sub>5</sub>)<sub>3</sub>PO]<sub>2</sub>XeO<sub>3 </sub>and (C<sub>5</sub>H<sub>5</sub>NO)<sub>3</sub>(XeO<sub>3</sub>)<sub>2</sub> are air-stable whereas [(CH<sub>3</sub>)<sub>2</sub>SO]<sub>3</sub>(XeO<sub>3</sub>)<sub>2</sub> slowly decomposes over several days and [(CH<sub>3</sub>)<sub>2</sub>CO]<sub>3</sub>XeO<sub>3</sub> undergoes adduct dissociation at room temperature. The xenon coordination sphere of [(C<sub>6</sub>H<sub>5</sub>)<sub>3</sub>PO]<sub>2</sub>XeO<sub>3</sub> is a distorted square pyramid which provides the first example of a five-coordinate XeO<sub>3</sub> adduct. The xenon coordination spheres of the remaining adducts are distorted octahedra comprised of three Xe---O secondary contacts that are approximately trans to the primary Xe–O bonds of XeO<sub>3</sub>. Quantum-chemical calculations were used to assess the Xe---O adduct bonds, which are predominantly electrostatic σ-hole bonds between the nucleophilic oxygen atoms of the bases and the σ-holes of the xenon atoms.

scholarly journals The internal conversion of gamma-rays.—Part II

1928 ◽  
Vol 121 (787) ◽  
pp. 447-456
Keyword(s):  
Magnetic Field ◽  
Quantum Mechanics ◽  
Wave Equation ◽  
Gamma Rays ◽  
Internal Conversion ◽  
Scalar Potential ◽  
X Ray ◽  
Electro Magnetic Field ◽  
Γ Rays ◽  
Electro Magnetic

In a previous paper the absorption of γ-rays in the K-X-ray levels of the atom in which they are emitted was calculated according to the Quantum Mechanics, supposing the γ-rays to be emitted from a doublet of moment f ( t ) at the centre of the atom. The non-relativity wave equation derived from the relativity wave equation for an electron of charge — ε moving in an electro-magnetic field of vector potential K and scalar potential V is h 2 ∇ 2 ϕ + 2μ ( ih ∂/∂ t + εV + ih ε/μ c (K. grad)) ϕ = 0. (1) Suppose, however, that K involves the space co-ordinates. Then, (K. grad) ϕ ≠ (grad . K) ϕ , and the expression (K . grad) ϕ is not Hermitic. Equation (1) cannot therefore be the correct non-relativity wave equation for a single electron in an electron agnetic field, and we must substitute h 2 ∇ 2 ϕ + 2μ ( ih ∂/∂ t + εV) ϕ + ih ε/ c ((K. grad) ϕ + (grad. K) ϕ ) = 0. (2)

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